{"title":"Spatial confounding in joint species distribution models","authors":"Francis K. C. Hui, Quan Vu, Mevin B. Hooten","doi":"10.1111/2041-210X.14420","DOIUrl":"10.1111/2041-210X.14420","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1906-1921"},"PeriodicalIF":6.3,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14420","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Robust characterisation of forest structure from airborne laser scanning—A systematic assessment and sample workflow for ecologists","authors":"Fabian Jörg Fischer, Toby Jackson, Grégoire Vincent, Tommaso Jucker","doi":"10.1111/2041-210X.14416","DOIUrl":"10.1111/2041-210X.14416","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1873-1888"},"PeriodicalIF":6.3,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14416","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142186080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Who is afraid of modelling time as a continuous variable?","authors":"Hanna Kokko","doi":"10.1111/2041-210X.14394","DOIUrl":"10.1111/2041-210X.14394","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1736-1756"},"PeriodicalIF":6.3,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14394","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K. M. Sumby, J. R. Stephen, J. J. Austin, R. K. Schilling, T. R. Cavagnaro
几十年来，在大学、政府机构和商业服务提供商的实验室中积累了为一系列研究和应用问题收集和分析的 DNA 档案样本。这些 DNA 档案是宝贵的基因组信息库，但在很大程度上尚未得到开发利用。随着高通量测序成本的降低和获取途径的增加，我们预测回溯性研究将会增加，以探索这些档案样本中蕴藏的丰富信息。然而，要做到这一点，我们需要对 DNA 样本的完整性有信心，因为这些样本通常是在不理想的条件下保存的，而且它们也不适合用于下游基因组分析。在此，我们借鉴古 DNA 中一个成熟的概念来评估样本的完整性，即冷冻 DNA 样本中恢复的扩增子信息含量的损失，并基于短线程和长线程 16S rRNA 基因序列的⍺-多样性比率。使用 PacBio 全长读数（V1-V9，1.5 kbp）和 Illumina 短读数（V3-V4，200-450 bp）对 2001 年至 2021 年期间从澳大利亚西部和南部农业区采集的 87 个从土壤中提取的储存 DNA 样本的 16S rRNA 可变区进行测序。当计算长读码和短读码的多样性比值以评估DNA降解情况时，年龄较大的样本与年龄较小的样本相比，多样性比值并没有降低。我们建议将此作为一种新方法，在利用档案 DNA 开展大规模多样性分析项目之前确认 DNA 的完整性。
{"title":"A novel method to assess the integrity of frozen archival DNA samples: Alpha-diversity ratios of short- and long-read 16S rRNA gene sequences","authors":"K. M. Sumby, J. R. Stephen, J. J. Austin, R. K. Schilling, T. R. Cavagnaro","doi":"10.1111/2041-210X.14411","DOIUrl":"10.1111/2041-210X.14411","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1804-1813"},"PeriodicalIF":6.3,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14411","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Discovering and measuring giant trees through the integration of multi-platform lidar data","authors":"Yu Ren, Hongcan Guan, Haitao Yang, Yanjun Su, Shengli Tao, Kai Cheng, Wenkai Li, Zekun Yang, Guoran Huang, Cheng Li, Guangcai Xu, Zhi Lu, Qinghua Guo","doi":"10.1111/2041-210X.14401","DOIUrl":"10.1111/2041-210X.14401","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1889-1905"},"PeriodicalIF":6.3,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14401","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142224325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aarne Hovi, Růžena Janoutová, Zbyněk Malenovský, Daniel Schraik, Jean-Philippe Gastellu-Etchegorry, Nicolas Lauret, Jan Novotný, Miina Rautiainen
模拟太阳辐射穿过林冠的光谱透射率的物理模型是研究短波辐射环境与林地生产力和生物多样性之间联系的有用工具。我们报告了对两种模拟森林冠层光谱透射率方法的综合评估。这两种方法分别是：(i) 由充满浑浊介质的单个树木组成的树冠中的三维辐射传递建模；(ii) 光子再碰撞概率理论（p 理论），并分别使用 DART-FT 和 PARAS 模型实现。模拟结果与中欧和北欧各地森林地块晴空条件下测得的树冠透射光谱的平均值和标准偏差进行了对比评估。总体而言，两个模型都与现场测量结果吻合。它们在针叶林中的表现相当，而在阔叶林中，PARAS 的精确度略低于 DART-FT。我们的结论是，在本研究测试的空间尺度上，这两种方法都能对树冠光谱透射率进行逼真的模拟，而且 p 理论是三维辐射传递的一种计算效率高、易于参数化的替代方法。
{"title":"Physically based modelling of spectral transmittance through forest canopies","authors":"Aarne Hovi, Růžena Janoutová, Zbyněk Malenovský, Daniel Schraik, Jean-Philippe Gastellu-Etchegorry, Nicolas Lauret, Jan Novotný, Miina Rautiainen","doi":"10.1111/2041-210X.14402","DOIUrl":"10.1111/2041-210X.14402","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1859-1872"},"PeriodicalIF":6.3,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14402","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
我们对生命历史的理解在很大程度上取决于时间校准，即为系统发育事件分配绝对时间的过程。贝叶斯方法对系统发育树进行时间标定的复杂性急剧增加，如今依赖于众多的方法选择。为所有这些选择找到客观的理由既困难又耗时。因此，通常只能在一个或少数几个参数条件下推断分异时间，而这些条件往往是任意选择的。要在构建稳健的生物时间尺度方面取得进展，就必须开发更好的方法来直观地量化结果对这些决定的敏感性。在这里，我们提出了一个 R 软件包，通过使用时间空间（即总结时间校准树所含节点年龄变化的图形表示法）来协助这项工作。我们使用 PhyloBayes 软件估算了三个经验数据集的分歧时间，从而进一步检验了这种方法。我们的结果表明，许多常见的方法学决定对推断年龄的影响存在很大差异，时钟（不相关与自相关）和位点的选择对推断年龄有很大影响。其他决定的影响相对较小，包括使用计算密集的位点异构模型 CAT-GTR，其影响可能只在极古老的分化（如最深的真核生物节点）中才能发现。chronospace 软件包实现了一系列图形和分析工具，有助于在推断发散时间时探索敏感性和计算资源的优先级。
{"title":"Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity","authors":"Nicolás Mongiardino Koch, Pablo Milla Carmona","doi":"10.1111/2041-210X.14404","DOIUrl":"10.1111/2041-210X.14404","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1822-1833"},"PeriodicalIF":6.3,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14404","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
一直以来，大多数昆虫时间生态学研究都使用直接观察、照相机或基于红外光束的监测器来量化定时间隔内的运动。虽然一些 DIY 替代系统比目前的标准运动活动监测器便宜，但这些方案的构建仍然复杂和/或计算密集。我们开发了成像运动活动监测器（iLAM），这是一种经济实惠（约 75 美元/台）的活动量化系统。iLAM 利用飞行笼内的 Raspberry Pi Zero W 计算机和夜视摄像机，以用户定义的时间间隔拍摄昆虫群体。开源的模块化 R 脚本处理图像，并输出一个文件，其中包含连续图像之间识别出的所有运动（blobs）的数量、大小、坐标位置和时间戳。输出结果可以直接进行分析，也可以转换成标准的 TriKinetics DAM 格式。我们通过比较不同昆虫物种（萤火虫：Photinus marginellus、P. greeni、P. obscurellus）、生态型（蛾：Ostrinia nubilalis）和性别（蛾：O. nubilalis）的昼夜活动，展示了 iLAM 系统的灵活性和强大功能。只有六台 iLAM（450 美元）采集到的数据表明，O. nubilalis 雌蛾的活动高峰期（AZT：19.2 小时）明显早于雄蛾（22.0 小时）。此外，来自单基因种群的雄蛾的内源期长度（AZT：21.3 小时）明显短于来自双基因背景的雄蛾（22.7 小时）。iLAM将成为研究人员测量不同物种、性别和种群在恒定和变化环境中的运动活动的重要工具。
{"title":"iLAM: Imaging Locomotor Activity Monitor for circadian phenotyping of large-bodied flying insects","authors":"Jacob N. Dayton, Avalon C. S. Owens","doi":"10.1111/2041-210X.14403","DOIUrl":"10.1111/2041-210X.14403","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 10","pages":"1814-1821"},"PeriodicalIF":6.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14403","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
生物定位是野生动物研究的核心，但如何将生物定位装置的影响降至最低仍是个问题。人们很少考虑生物除害装置对动物质心（COM）的影响以及由此造成的飞行控制和稳定性损失。我们运用已确立的航空原理，估算了飞行中的鸟类或蝙蝠在颈部、背部、臀部或尾部放置生物装载装置的典型位置可能对其质心（COM）产生的影响。然后，我们采用航空航天工程学中修改过的阈值来估算 COM 的变化会导致飞行控制和稳定性发生与体能相关的改变的极限值。通用模型说明了影响飞行控制和稳定性的生物锚定装置的位置和质量之间的权衡。七个针对特定物种的例子表明，对不同体型和体质的动物来说，改变COM所造成的后果存在很大差异。将装置放置在尾部总是导致最大的 COM 变化，而放置在背部中央则导致最小的变化。有些人将生物定位装置的重量阈值定为 5%，这在稳定性方面几乎没有误差余地，很容易导致 COM 发生危险的变化。其他人使用的 3% 重量阈值导致的 COM 变化要小得多，但在远离自然 COM 的情况下，仍会影响飞行控制和稳定性。有兴趣最大限度地减少对野生动物健康影响的研究人员在安装生物定位装置时应考虑重量、平衡和 COM。装置离自然 COM 越远，相对于动物的质量就应该越小。
{"title":"A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats","authors":"Todd E. Katzner, George S. Young","doi":"10.1111/2041-210X.14400","DOIUrl":"10.1111/2041-210X.14400","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 9","pages":"1553-1560"},"PeriodicalIF":6.3,"publicationDate":"2024-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14400","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Adaptive sampling in ecology: Key challenges and future opportunities","authors":"Peter A. Henrys, Thomas O. Mondain-Monval, Susan G. Jarvis","doi":"10.1111/2041-210X.14393","DOIUrl":"10.1111/2041-210X.14393","url":null,"abstract":"<p>\u0000 \u0000 </p>","PeriodicalId":208,"journal":{"name":"Methods in Ecology and Evolution","volume":"15 9","pages":"1483-1496"},"PeriodicalIF":6.3,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.14393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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